1     M         0.507   0.519   0.527   1.015   0.995   0.939   0.516   0.533   0.545
2     D         0.507   0.519   0.527   0.810   0.779   0.784   0.516   0.533   0.545
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     N        -3.704  -3.229  -2.957  -3.350  -2.768  -2.386  -3.271  -2.759  -2.459
5     K         0.507   0.519   0.527   0.752   0.748   0.740   0.516   0.533   0.545
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     T        -2.277  -2.378  -2.229  -2.216  -2.428  -2.287  -2.177  -2.310  -2.120
8     P         0.507   0.519   0.527   1.015   0.995   0.939   0.516   0.533   0.545
9     V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
10    T        -1.504  -1.419  -1.212  -1.656  -1.559  -1.224  -1.840  -1.737  -1.453
11    L         0.507   0.519   0.527   0.516   0.551   0.562   0.516   0.533   0.545
12    A        -0.427  -0.867  -1.193   0.135  -0.556  -1.350  -0.325  -0.902  -1.422
13    K        -0.947  -0.615  -1.187  -0.815  -0.364  -1.494  -0.999  -0.563  -1.413
14    V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
15    I        -1.334  -1.866  -2.221  -0.703  -1.507  -2.311  -1.083  -1.702  -2.111
16    K        -0.427  -0.867  -1.193  -0.069  -0.761  -1.515  -0.325  -0.902  -1.422
17    V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
18    L         0.507   0.519   0.527   0.516   0.551   0.562   0.516   0.533   0.545
19    G         0.507   0.519   0.527   0.623   0.643   0.643   0.516   0.533   0.545
20    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
21    T         0.507   0.519   0.527   0.635   0.698   0.652   0.516   0.533   0.545
22    G         0.507   0.519   0.527   0.623   0.643   0.643   0.516   0.533   0.545
23    S         0.507   0.519   0.527   0.833   0.812   0.802   0.516   0.533   0.545
24    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
25    G         0.507   0.519   0.527   0.623   0.643   0.643   0.516   0.533   0.545
26    G         0.507   0.519   0.527   0.623   0.643   0.643   0.516   0.533   0.545
27    V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
28    T         0.507   0.519   0.527   0.635   0.698   0.652   0.516   0.533   0.545
29    Q         0.507   0.519   0.527   1.127   1.084   1.024   0.516   0.533   0.545
30    V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
31    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
32    V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
33    E         0.507   0.519   0.527   0.540   0.582   0.580   0.516   0.533   0.545
34    F         0.507   0.519   0.527   1.138   1.106   1.032   0.516   0.533   0.545
35    L        -2.131  -2.240  -2.232  -1.949  -2.093  -1.966  -2.093  -2.199  -2.123
36    E        -1.504  -1.419  -1.212  -1.709  -1.615  -1.239  -1.840  -1.737  -1.453
37    D         0.507   0.519   0.527   0.810   0.779   0.784   0.516   0.533   0.545
38    T        -2.931  -2.998  -2.950  -2.503  -2.527  -2.459  -2.598  -2.547  -2.454
39    S        -0.947  -1.152  -1.214  -0.586  -0.993  -1.183  -0.999  -1.317  -1.456
40    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
41    T        -1.504  -1.419  -1.212  -1.614  -1.511  -1.177  -1.840  -1.737  -1.453
42    I         0.507   0.519   0.527   0.867   0.861   0.828   0.516   0.533   0.545
43    V        -1.290  -1.352  -1.212  -1.850  -1.912  -1.532  -1.504  -1.628  -1.452
44    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
45    N         0.507   0.519   0.527   1.026   1.026   0.948   0.516   0.533   0.545
46    V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
47    K         0.507   0.519   0.527   0.752   0.748   0.740   0.516   0.533   0.545
48    G         0.507   0.519   0.527   0.623   0.643   0.643   0.516   0.533   0.545
49    P         0.507   0.519   0.527   1.015   0.995   0.939   0.516   0.533   0.545
50    V         0.507   0.519   0.527  -0.004   0.070   0.170   0.516   0.533   0.545
51    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
52    E         0.507   0.519   0.527   0.540   0.582   0.580   0.516   0.533   0.545
53    N        -2.131  -2.056  -2.229  -1.595  -1.687  -1.915  -2.093  -2.046  -2.120
54    D         0.507   0.519   0.527   0.810   0.779   0.784   0.516   0.533   0.545
55    I         0.507   0.519   0.527   0.867   0.861   0.828   0.516   0.533   0.545
56    L         0.507   0.519   0.527   0.516   0.551   0.562   0.516   0.533   0.545
57    V        -1.504  -1.246  -1.210  -1.962  -1.611  -1.338  -1.840  -1.462  -1.450
58    L         0.507   0.519   0.527   0.516   0.551   0.562   0.516   0.533   0.545
59    M        -1.290  -1.352  -1.212  -1.003  -1.285  -1.130  -1.504  -1.628  -1.452
60    E         0.507   0.519   0.527   0.540   0.582   0.580   0.516   0.533   0.545
61    S         0.507   0.519   0.527   0.833   0.812   0.802   0.516   0.533   0.545
62    E         0.507   0.519   0.527   0.540   0.582   0.580   0.516   0.533   0.545
63    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
64    E         0.507   0.519   0.527   0.540   0.582   0.580   0.516   0.533   0.545
65    A         0.507   0.519   0.527   0.947   0.937   0.888   0.516   0.533   0.545
66    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
67    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
68    L         0.507   0.519   0.527   0.516   0.551   0.562   0.516   0.533   0.545
69    R         0.507   0.519   0.527  -0.081   0.002   0.112   0.516   0.533   0.545
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/Q3E7X9
Output conservation file - output/Q3E7X9
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
